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1. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Author

Wong, Gane Ka-Shu, Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, Meng, Qingshun, Zhou, Jun, Li, Dawei, Zhang, Jingjing, Ni, Peixiang, Li, Songgang, Ran, Longhua, Li, Heng, Zhang, Jianguo, Li, Ruiqiang, Li, Shengting, Zheng, Hongkun, Lin, Wei, Li, Guangyuan, Wang, Xiaoling, Zhao, Wenming, Li, Jun, Ye, Chen, Dai, Mingtao, Ruan, Jue, Zhou, Yan, Li, Yuanzhe, He, Ximiao, Zhang, Yunze, Wang, Jing, Huang, Xiangang, Tong, Wei, Chen, Jie, Ye, Jia, Chen, Chen, Wei, Ning, Li, Guoqing, Dong, Le, Lan, Fengdi, Sun, Yongqiao, Zhang, Zhenpeng, Yang, Zheng, Yu, Yingpu, Huang, Yanqing, He, Dandan, Xi, Yan, Wei, Dong, Qi, Qiuhui, Li, Wenjie, Shi, Jianping, Wang, Miaoheng, Xie, Fei, Wang, Jianjun, Zhang, Xiaowei, Wang, Pei, Zhao, Yiqiang, Li, Ning, Yang, Ning, Dong, Wei, Hu, Songnian, Zeng, Changqing, Zheng, Weimou, Hao, Bailin, Hillier, Ladeana W, Yang, Shiaw-Pyng, Warren, Wesley C, Wilson, Richard K, Brandström, Mikael, Ellegren, Hans, Crooijmans, Richard P M A, van der Poel, Jan J, Bovenhuis, Henk, Groenen, Martien A M, Ovcharenko, Ivan, Gordon, Laurie, Stubbs, Lisa, Lucas, Susan, Glavina, Tijana, Aerts, Andrea, Kaiser, Pete, Rothwell, Lisa, Young, John R, Rogers, Sally, Walker, Brian A, van Hateren, Andy, Kaufman, Jim, Bumstead, Nat, Lamont, Susan J, Zhou, Huaijun, Hocking, Paul M, Morrice, David, de Koning, Dirk-Jan, Law, Andy, Bartley, Neil, Burt, David W, Hunt, Henry, Cheng, Hans H, Gunnarsson, Ulrika, Wahlberg, Per, Andersson, Leif, Kindlund, Ellen, Tammi, Martti T, Andersson, Björn, Webber, Caleb, Ponting, Chris P, Overton, Ian M, Boardman, Paul E, Tang, Haizhou, Hubbard, Simon J, Wilson, Stuart A, Yu, Jun, Wang, Jian, Yang, Huanming, Wong, Gane Ka-Shu, Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, Meng, Qingshun, Zhou, Jun, Li, Dawei, Zhang, Jingjing, Ni, Peixiang, Li, Songgang, Ran, Longhua, Li, Heng, Zhang, Jianguo, Li, Ruiqiang, Li, Shengting, Zheng, Hongkun, Lin, Wei, Li, Guangyuan, Wang, Xiaoling, Zhao, Wenming, Li, Jun, Ye, Chen, Dai, Mingtao, Ruan, Jue, Zhou, Yan, Li, Yuanzhe, He, Ximiao, Zhang, Yunze, Wang, Jing, Huang, Xiangang, Tong, Wei, Chen, Jie, Ye, Jia, Chen, Chen, Wei, Ning, Li, Guoqing, Dong, Le, Lan, Fengdi, Sun, Yongqiao, Zhang, Zhenpeng, Yang, Zheng, Yu, Yingpu, Huang, Yanqing, He, Dandan, Xi, Yan, Wei, Dong, Qi, Qiuhui, Li, Wenjie, Shi, Jianping, Wang, Miaoheng, Xie, Fei, Wang, Jianjun, Zhang, Xiaowei, Wang, Pei, Zhao, Yiqiang, Li, Ning, Yang, Ning, Dong, Wei, Hu, Songnian, Zeng, Changqing, Zheng, Weimou, Hao, Bailin, Hillier, Ladeana W, Yang, Shiaw-Pyng, Warren, Wesley C, Wilson, Richard K, Brandström, Mikael, Ellegren, Hans, Crooijmans, Richard P M A, van der Poel, Jan J, Bovenhuis, Henk, Groenen, Martien A M, Ovcharenko, Ivan, Gordon, Laurie, Stubbs, Lisa, Lucas, Susan, Glavina, Tijana, Aerts, Andrea, Kaiser, Pete, Rothwell, Lisa, Young, John R, Rogers, Sally, Walker, Brian A, van Hateren, Andy, Kaufman, Jim, Bumstead, Nat, Lamont, Susan J, Zhou, Huaijun, Hocking, Paul M, Morrice, David, de Koning, Dirk-Jan, Law, Andy, Bartley, Neil, Burt, David W, Hunt, Henry, Cheng, Hans H, Gunnarsson, Ulrika, Wahlberg, Per, Andersson, Leif, Kindlund, Ellen, Tammi, Martti T, Andersson, Björn, Webber, Caleb, Ponting, Chris P, Overton, Ian M, Boardman, Paul E, Tang, Haizhou, Hubbard, Simon J, Wilson, Stuart A, Yu, Jun, Wang, Jian, and Yang, Huanming

Published
2004

2. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Author

Wong GK, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Dai M, Ruan J, Zhou Y, Li Y, He X, Zhang Y, Wang J, Huang X, Tong W, Chen J, Ye J, Chen C, Wei N, Li G, Dong L, Lan F, Sun Y, Zhang Z, Yang Z, Yu Y, Huang Y, He D, Xi Y, Wei D, Qi Q, Li W, Shi J, Wang M, Xie F, Wang J, Zhang X, Wang P, Zhao Y, Li N, Yang N, Dong W, Hu S, Zeng C, Zheng W, Hao B, Hillier LW, Yang SP, Warren WC, Wilson RK, Brandström M, Ellegren H, Crooijmans RP, van der Poel JJ, Bovenhuis H, Groenen MA, Ovcharenko I, Gordon L, Stubbs L, Lucas S, Glavina T, Aerts A, Kaiser P, Rothwell L, Young JR, Rogers S, Walker BA, van Hateren A, Kaufman J, Bumstead N, Lamont SJ, Zhou H, Hocking PM, Morrice D, de Koning DJ, Law A, Bartley N, Burt DW, Hunt H, Cheng HH, Gunnarsson U, Wahlberg P, Andersson L, Kindlund E, Tammi MT, Andersson B, Webber C, Ponting CP, Overton IM, Boardman PE, Tang H, Hubbard SJ, Wilson SA, Yu J, Wang J, and Yang H

Subjects
Alleles, Amino Acid Sequence, Animals, Animals, Domestic classification, Animals, Domestic genetics, Chickens classification, Chromosomes genetics, Female, Haplotypes genetics, Humans, Molecular Sequence Data, Ornithine Carbamoyltransferase chemistry, Selection, Genetic, Chickens genetics, Genome, Genomics, Physical Chromosome Mapping, Polymorphism, Single Nucleotide genetics
Abstract

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.

Published
2004
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